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updated getting started file

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docs/Examples/1_getting_started.ipynb
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"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"# REEPS Tutorial - Getting started\n", "# LLEPE Tutorial - Getting started\n",
"## Introduction\n", "## Introduction\n",
"In this notebook, you will learn how to use REEPS to fit thermodynamic parameters to experimental data and explore how well the parameters fit.\n", "In this notebook, you will learn how to use LLEPE to fit thermodynamic parameters to experimental data and explore how well the parameters fit.\n",
"## Installation\n", "## Installation\n",
"Create a conda environment with the following command. The environment name in this example is \"thermo_env\". <br/> \n",
"```$ conda create --name thermo_env python=3.7```<br/>\n",
"Then run the following line to activate the environment"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"```$ conda activate thermo_env```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"In your terminal run<br/>\n", "In your terminal run<br/>\n",
"```$ git clone https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git```<br/>\n", "```$ git clone https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git```<br/>\n",
"Navigate into the folder with <br/>\n", "Navigate into the folder with <br/>\n",
"```$ cd parameter-estimation```<br/>\n", "```$ cd parameter-estimation```<br/>\n",
"And run <br/>\n", "And run <br/>\n",
"```pip install -e.```<br/>\n", "```pip install -e.```<br/>"
"\n"
] ]
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"## Import and instantiate REEPS" "## Import and instantiate LLEPE"
] ]
}, },
{ {
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"First, you will need to import the package and instantiate REEPS with a few parameters." "First, you will need to import the package and instantiate LLEPE with a few parameters."
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 1, "execution_count": 1,
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'llepe'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-1-2c8cdd51efc7>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mllepe\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLLEPE\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2\u001b[0m opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species',\n\u001b[1;32m 3\u001b[0m \u001b[0;34m'upper_attrib_name'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'name'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;34m'upper_attrib_value'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'Nd(H(A)2)3(org)'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;34m'lower_element_name'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'h0'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'llepe'"
]
}
],
"source": [ "source": [
"from reeps import REEPS\n", "from llepe import LLEPE\n",
"searcher_parameters = {'exp_csv_filename': '../../data/csvs/Nd_exp_data.csv',\n", "opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species',\n",
" 'upper_attrib_name': 'name',\n",
" 'upper_attrib_value': 'Nd(H(A)2)3(org)',\n",
" 'lower_element_name': 'h0',\n",
" 'lower_attrib_name': None,\n",
" 'lower_attrib_value': None,\n",
" 'input_format': '{0}',\n",
" 'input_value': -4.7e6}}\n",
"llepe_parameters = {'exp_csv_filename': '../../data/csvs/Nd_exp_data.csv',\n",
" 'phases_xml_filename': '../../data/xmls/twophase.xml',\n", " 'phases_xml_filename': '../../data/xmls/twophase.xml',\n",
" 'opt_dict': {'Nd(H(A)2)3(org)': {'h0': -4.7e6}},\n", " 'opt_dict': opt_dict,\n",
" 'phase_names': ['HCl_electrolyte', 'PC88A_liquid'],\n", " 'phase_names': ['HCl_electrolyte', 'PC88A_liquid'],\n",
" 'aq_solvent_name': 'H2O(L)',\n", " 'aq_solvent_name': 'H2O(L)',\n",
" 'extractant_name': '(HA)2(org)',\n", " 'extractant_name': '(HA)2(org)',\n",
" 'diluant_name': 'dodecane',\n", " 'diluant_name': 'dodecane',\n",
" 'complex_names': ['Nd(H(A)2)3(org)'],\n", " 'complex_names': ['Nd(H(A)2)3(org)'],\n",
" 'rare_earth_ion_names': ['Nd+++'],\n", " 'extracted_species_ion_names': ['Nd+++'],\n",
" 'aq_solvent_rho': 1000.0,\n", " 'aq_solvent_rho': 1000.0,\n",
" 'extractant_rho': 960.0,\n", " 'extractant_rho': 960.0,\n",
" 'diluant_rho': 750.0}\n", " 'diluant_rho': 750.0}\n",
"searcher = REEPS(**searcher_parameters)" "estimator = LLEPE(**llepe_parameters)"
] ]
}, },
{ {
@ -72,7 +107,7 @@
"metadata": {}, "metadata": {},
"source": [ "source": [
"exp_csv_filename is the file name for the csv containing experimental data. <br/>\n", "exp_csv_filename is the file name for the csv containing experimental data. <br/>\n",
"Let us get the pandas dataframe created by REEPS." "Let us get the pandas dataframe created by LLEPE."
] ]
}, },
{ {
@ -188,7 +223,7 @@
"metadata": {}, "metadata": {},
"source": [ "source": [
"The rows are for experiments, and the columns are for the measured quantaties. <br/>\n", "The rows are for experiments, and the columns are for the measured quantaties. <br/>\n",
"REEPS is looking for the ordering of these columns so it is important your experimental file has this ordering. Column names do not matter.<br/>\n", "LLEPE is looking for the ordering of these columns so it is important your experimental file has this ordering. Column names do not matter.<br/>\n",
"Below is a table explaining the meaning of the column headers and the needed column order.<br/>\n", "Below is a table explaining the meaning of the column headers and the needed column order.<br/>\n",
"If you have more than one rare earth element, append the data to the end in the same order (aq_i, aq_eq, d_eq)" "If you have more than one rare earth element, append the data to the end in the same order (aq_i, aq_eq, d_eq)"
] ]
@ -522,7 +557,7 @@
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3", "pygments_lexer": "ipython3",
"version": "3.7.7" "version": "3.7.5"
} }
}, },
"nbformat": 4, "nbformat": 4,

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